OpenPMD standard for simulation data (and metadata) further developed in PaNOSC WP5
Standardized formatting and hierarchical organization of simulation data and associated metadata is paramount to support seamless exchange of data between simulation software in simulation pipelines and to benefit from third party data visualization and analysis software that support these formats. In the frame of PaNOSC WP5 – Virtual Neutron and X-ray laboratory, metadata standard extensions for simulation data have been developed by applying openPMD (Open Particle and Mesh Data) standard to all simulated data in the work package. This step has allowed the wavefront data, raytracing particle data, and atomic configuration data produced by each start-to-end simulation module to become accessible, inter-operable and reusable, in line with the core concepts of the FAIR data principles. In particular, domain specific extensions have been developed for the simulation stages of start-to-end photon and neutron experiment simulations, and namely: - Simulations of coherent wavefront propagation – Simulation of coherent lightsources and beam transport. Applications include studying the intensity and phase distribution at the experimental interaction point and effects of misalignments, pointing errors, fluctuations in the temporal, spatial and spectral pulse structure on observable signals and sample reconstruction. This domain extension can be found here: https://github.com/PaNOSC-ViNYL/openPMD-standard/blob/upcoming-2.0.0/EXT_WAVEFRONT.md - Neutron raytracing simulations for design of instrumentation – Such simulations provide a phase-space description of the neutron beam at the sample position, and also allow doing virtual experiments that include the sample physics resulting in expected intensity on the detector. The openPMD extension for neutron raytracing simulations contains the necessary fields for describing neutron state (including position, velocity, polarization, weight and time), facilitating transfer of neutron rays between different simulation tools. The domain extension for neutron scattering can be found here: https://github.com/PaNOSC-ViNYL/openPMD-standard/blob/upcoming-2.0.0/EXT_NRAYTRACING.md - Photon raytracing simulations used in the design and performance assessment of X-ray beamlines. Raytracing allows simulation of different properties of the beam, such as the spot size, divergence and generally propagate rays through the beamline. The openPMD extension for X-ray/photon raytracing contains all the necessary information for the use of interoperable codes (e.g. SIMEX), and a common data format. The domain extension can be found here: https://github.com/PaNOSC-ViNYL/openPMD-standard/blob/upcoming-2.0.0/EXT_PRAYTRACE.md - Molecular Dynamics (MD) data simulations, to analyse atom/molecular movements. MD is broadly used in statistical physics, physical chemistry, structural biology, materials science and crystallography. This tool is extremely useful to predict the response of a molecular system to external fields, as well as to probes such as photon or neutron beams. The domain extension can be found here: https://github.com/PaNOSC-ViNYL/openPMD-standard/blob/upcoming-2.0.0/EXT_MD.md The openPMD standard developed in the WP defines a number of mandatory and optional metadata information to define and specify the physical meaning of the data, allowing wide adoption in numerous simulation codes, visualization codes and simulation workflow platforms. Find the link to the developed standard here: https://github.com/PaNOSC-ViNYL/openPMD-standard/tree/upcoming-2.0.0 Download the deliverable here: https://www.panosc.eu/wp-content/uploads/2019/12/D5.1-Prototype-Simulation-Data-format.pdf
Keywords
EOSC, OpenPMD, Simulation Data, European Open Science Cloud, PaNOSC, photon science, neutron science, FAIR data
